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Records from this period are fragmented, but what is known is that the wars' roots lie in a group of Human scientists' ambitious attempt to improve the race through selective breeding and genetic engineering. They created a race of "supermen," popularly known as the Augments, who were mentally and physically superior to ordinary men and women. They were five times stronger than the average person, their lung efficiency was 50 percent better than normal, and their intelligence was double that of normal Humans. They also had enhanced senses, including an ability to hear beyond that of Human capabilities. (TOS: "Space Seed"; ENT: "Borderland", "Cold Station 12")

The Augments were created by the scientists in the 1950scold war era in the hopes that they would lead Humanity into an era of peace in a world that had only known war. (Star Trek Into Darkness) One aspect these scientists overlooked was the personality of the Augments. Along with their superior abilities, the Augments were aggressive and arrogant, flaws which the scientists were unable to correct at the time, due to the infancy of the science. One of the Augments' creators realized this, writing that "superior ability breeds superior ambition." That same scientist was ultimately killed by one of his own creations. (TOS: "Space Seed"; ENT: "Cold Station 12", "The Augments")

The Augments rose to power and held dominance over a large portion of Humanity, beginning in the early 1990s. Among the most notorious of these superhuman conquerors was Khan Noonien Singh, who in 1992 became the "absolute ruler" of more than a quarter of the planet, from Asia through the Middle East. (TOS: "Space Seed")

The following year, a group of fellow "supermen" followed in Khan's footsteps, and simultaneously seized power in over 40 nations. Some people were treated as little more than slaves by the Augments. Khan considered himself a prince "with power over millions," and unlike some other nations ruled by Augments, under his rule there were no massacres and no wars of aggression until he was attacked; he was thus among the most admired of the so-called "tyrants" into the 23rd century, being called the "best of the tyrants" by James T. Kirk. (TOS: "Space Seed"; Star Trek II: The Wrath of Khan; ENT: "Borderland")

Reports as to exactly how the wars began vary; some claim that humanity rose up against Khan and his fellow "supermen," while others believe the Augments began to fight among themselves. Regardless of how they began, or who started them, the Eugenics Wars had a devastating impact on Earth, as entire populations were bombed out of existence. (ENT: "Cold Station 12"; TOS: "Space Seed")

Among the areas affected by the wars was North Africa. One conflict that occurred there involved a battalion of soldiers that included the great-grandfather of future StarfleetCaptainJonathan Archer. In this encounter, Archer's great-grandfather was able to convince the commander of his enemy's forces to hold their fire long enough to evacuate a school that was directly between them. (ENT: "Hatchery")

The Augments were eventually defeated by Humans who were not genetically enhanced. Khan was the last of the tyrants to be overthrown, in 1996. Khan and over eighty of the "supermen" were condemned to die as war criminals. They however went unaccounted for, a fact the governments of the time did not disclose to the public in order to prevent panic. Rumors were later on confirmed in the 23rd century, that Khan and 84 of his followers had managed to flee the planet unattended aboard an early sleeper ship, the SS Botany Bay. (TOS: "Space Seed"; Star Trek II: The Wrath of Khan; Star Trek Into Darkness)

While the Eugenics Wars were a set of global conflicts, some cities appeared to have survived the war seemingly unaffected, such as Los Angeles that was seen in VOY: "Future's End" during the same year the wars had ended, 1996.

As both conflicts were fought over the issue of genetic manipulation, this suggests the Eugenics Wars was regarded as the initial cause and prelude for the Third World War, much like how the Second World War is often seen as a result of the First.

Doctor Keniclius

Soong and the Augment embryos

Genetic engineering of Humans was ultimately banned on Earth, as the concept was considered anti-Humanistic by Earth leaders. As a result of this, Doctor Stavos Keniclius was exiled from his community, which eventually led him to depart Earth permanently. The ban was placed primarily as an attempt to prevent another event like the Eugenics Wars, and to ensure that Humanity did not endure the wrath of another Khan Noonien Singh-type tyrant. (TAS: "The Infinite Vulcan"; DS9: "Doctor Bashir, I Presume", "Statistical Probabilities")

The ban on genetic engineering was challenged by the geneticist Arik Soong in the 2130s, when he stole some of the Augment embryos left over from the wars, which were being stored at Cold Station 12. Soong believed that genetic engineering was the key to improving Humankind and preventing illness, and that it should be given another chance. By raising the Augments himself, Soong believed he could prevent them from behaving like their brethren from the Eugenics Wars. His plan failed as the aggressive nature of the Augments took dominance, and they threatened to incite war and cause mass murder. Earth Starfleet's mission to hunt down and capture the renegade "supermen" ultimately led to the destruction of the Augments, as well as most of the embryos. (ENT: "Borderland", "Cold Station 12", "The Augments")

Not all of the embryos were destroyed, though. Some found their way into the hands of Klingons who, believing Humans were improving themselves in order to conquer the Klingon Empire, attempted to use the DNA from the embryos to enhance themselves. The end result was a mutation of a highly-contagious virus that caused massive changes in physical appearance, biological structure, and even basic personality traits of large portions of the Klingon race. (ENT: "Affliction", "Divergence")

In "Space Seed", Spock describes the Eugenics Wars as "the era of your last so-called world war," suggesting this conflict could be World War III. In TOS: "Bread and Circuses", it is stated by Spock that 37 million died in World War III – consistent with Phlox's assertion that over 30 million died in the Eugenics Wars (again connecting World War III and the Eugenics Wars) – but not Riker's claim that 600 million died in the nuclear conflict in the 2050s. As Spock was speaking in the context of despotism, and what constitutes despotic "responsibility" is open to interpretation, his statement may not give the total death count.

In TNG: "Up The Long Ladder", Data stated that Humans were still recovering from the effects of World War III in the early 22nd century. This statement makes more sense within the context of a mid 21st century war than that of a late 20th century war, suggesting that World War III and the Eugenics Wars are not the same conflict, as confirmed in Star Trek: First Contact.

The Star Trek: The Eugenics Wars books portray a different view on the Eugenics Wars as being a more covert hidden battle between the genetically engineered "supermen" rather than an overt one in an attempt to marry the original dates of the Eugenics Wars with the events of the present day. It also raises the quite logical hypothesis that Gary Seven was involved in the overthrow of Khan and the other tyrants since he conceivably was present on Earth at the time of Khan's birth and would have known or seen the advent of the eugenics movement. Numerous 20th Century Trek characters appear in the story, including Rain Robinson (who at the end of the second book becomes Roberta Lincoln's assistant), Ralph Offenhouse (an early financial backer of the genetic engineering program), Clare Raymond (her death is not an embolism but collateral damage from a nerve gas attack, Khan's assassination of Vasily Hunyadi, the fellow Augment secretly behind the Balkan conflicts of the early 1990s), Gillian Taylor, Flint (as "Wilson Evergreen"), and Jeff Carlson, who designed the Botany Bay - with Shannon O'Donnell and Walter Nichols involved in the project - primarily with technology reverse-engineered from Quark's Treasure.

In the Star Trek: Khan comic book series associated with the Abramsverse, the creative team went with a portrayal of the wars as being an open conflict that outright affected the whole planet.

In "The Rules of War", a short story from the anthology Strange New Worlds 9, the enemy commander whom Archer's great-grandfather Nathan Archer negotiated with in North Africa is Stavos Keniclius.